Wyniki wyszukiwania - BazTech

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Towards mechanisms of nanotoxicity - interaction of gold nanoparticles with proteins and DNA

Krupa P., Mozolewska M. A., Rasulev B., Czaplewski C., Leszczyński J.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2014

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Vol. 18, No 4

337--341

EN

Even though most of the existing studies of gold nanoparticles indicate that they are safe to use, some researchers show that specific forms of nanoparticles (e.g. nanorods) are able to destroy the cell membrane and very small nanoparticles (below 37nm in diameter) in high concentration have been deadly for mice. We used the Amber12 package to perform a series of molecular dynamics (MD) simulations of gold nanoparticles with various small proteins important for the human body and a DNA molecule to determine the interactions and consequently the possible toxicity of gold clusters. Lennard-Jones interactions were used to simulate the behavior of gold nanoparticles with biomacromolecules in water with an optimal set of parameters (selected based on a comparison of MD structures and structures computed by DFT). Gold nanoparticle structures were obtained as a result of MD simulations from an initial structure, where gold atoms were at a distance of 10 ̊ A from one another. A predicted BDNA structure of a palindromic sequence‘ CGCATGAGTACGC ’ and a 2 JYK molecule were used as representatives of the DNA molecule. The preliminary results show that, in particular small gold nanoparticle s, interact strongly with proteins and DNA by creating stable complexes, which can then cause harmful reactions to the human body when present in high concentration.

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The ECEPP package for conformational analysis of polypeptides

Ripoll D. R., Liwo A., Czaplewski C.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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1999

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Vol. 3, No 3

313-331

EN

We present here the ECEPPAK (developed in the laboratory of prof. H.A. Scheraga, Cornell University) and ANALYZE packages for the conformational search of polypeptides that is based on the ECEPP/3 force field. The functions of the program include energy calculation and minimization and global conformational search using the Electrostatically Driven Monte Carlo (EDMC) method. The search can be constrained using experimental information e.g., the distance constraints from NMR measurements. The sister program, ANALYZE, allows the user to classify the conformations by means of cluster analysis and fit the statistical weights of the conformations to best fit the experimental observables. The package is extensively parallelized, which allows the user to carry out the conformational search even of comparatively large polypeptides in real time.

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Cyclic Analogues of Proline-Rich Protein Fragments : Part II : Conformational Studies Using NMR Spectroscopy and Theoretical Conformational Analysis

Rodziewicz S., Wirkus-Romanowska I., Ciurak M., Miecznikowska H., Kupryszewski G., Czaplewski C., Liwo A., Rolka K.

Polish Journal of Chemistry

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1999

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Vol. 73, nr 10

1697-1710

EN

These peptides were designed based on the immunoregulatory activity of linear peptides obtained after chymotrypsin digestion of PRP. Despite the fact that the structures of both analogues cannot be interpreted in terms of a single conformation, the superposition of the most populated conformations of the cyclic peptides studied revealed a similar geometry for the Tyr-Val-pro-Leu-Phe-Pro fragment (RMSD=1.6 A) in both peptides and therefore might be considered to be responsible for the biological activity.

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Receptory sprzężone z białkami G (GPCR) ; struktura i oddziaływania z bioligandami

Ciarkowski J., Czaplewski C., Kaźmierkiewicz R., Politowska E.

Wiadomości Chemiczne

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1998

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[Z] 52, 5-6

431-447

EN

G protein-coupled receptors (GPCRs) from the largest superfamily, having over 1000 members, of integral membrane proteins sharing the following features: (i) All members from 7 hydrophobic a-helices of ~38 A (25 amino acids, 7 turns) along a single chain. The consecutive helices pass the membrane forth and back, starting from the extracellular side, to from a heptahelical transmembrane domain. This arrangement implicates 6 interhelical loops, whereof the even ones plus the N-terminus create the receptor's extracellular domain while the odd ones plus the C-terminus from its intracellular domain. (ii) All GPCRs are stimulated by extracellular signals of miscellaneous character. (iii) Stimulated GPCRs pass the extracellular signal via their transmembrane and intracellular domains to the cytosolic peripheral heterotrimeric GTP/GDP - binding proteins (G proteins), mediating the signal's further transduction to various cellular second messenger systems. A current status of structural studies on GPCRs, consisting of low ~7.5 A resolution experimental structures and supplementary molecular modelling, is presented. Subsequently, some results of author's own work on modelling essential interactions between the V2 vaasopressin renal receptor (V2R) and its agonists [Arg8] Vasopressin (AVP), [d-Arg8] Vasopressin (DAVP), and both the peptide desGly9 -[Mca1, D-Ile2, Ile4]AVP and the nonpeptide antagonist OPC-31260, are discussed. Finally perspectives for future developments are outlined.

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Theoretical study of proton-transfer energy surfaces in small water clusters and cubic ice

Czaplewski C.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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1998

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Vol. 2, No 1

31-45

EN

The energetics of proton transfer in water clusters consisting of two to six molecules and in cubic ice was analyzed in detail using both Hartree Fock and gradient-corrected density functional theory. Since the energy of the ion-pair structure created by proton transfer is always higher than that of the neutral water structure grid calculations and constrained geometry optimization are needed. In the case of cubic ice various arrangements of the hydrogen atoms on a fixed oxygen lattice were investigated. In this system proton transfer leads to the creation of ionic point defects which are saddle points on the potential energy surface.

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Targets for majority of drugs: G protein-coupled receptors - their structure and interaction with bioligands

Ciarkowski J., Czaplewski C., Pasenkiewicz-Gierula M.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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1998

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Vol. 2, No 4

583-599

EN

G protein-coupled receptors (GPCRs) are the most frequent targets for many drugs. They form the largest superfamily of integral membrane proteins, of which more than 1000 members have the following common features: (i) All GPCRs form 7 hydrophobic a-helices of length ~38A (25 amino acids, 7 turns) along a single chain. The consecutive helices alternatively cross the membrane, starting from the extracellular side, so that they form a heptahelical transmembrane domain interwoven with 6 loops, of which the even ones plus the N-terminus create the receptor's extracellular domain while the odd ones plus the C-terminus form its intracellular domain. (ii) All GPCRs are stimulated by diverse extracellular (primary) signals. (iii) Stimulated GPCRs convey the primary signals via their transmembrane and intracellular domains to the cytosolic peripheral heterotrimeric GTP-binding proteins (G proteins), mediating the signal's further transduction to various cellular second messenger systems. A current status of structural studies on GPCRs, consisting of low ~7.5A resolution experimental structures and supplementary molecular modeling, is outlined. Subsequently, some results of authors' own work on studying essential interactions of the V2 vasopressin renal receptor (V2R) with its agonist [Arg8]Vasopressin (AVP) and selected antagonists are presented, as well as their possible impact on the biological signal transduction is discussed. Finally, perspectives for future developments are sketched.